Whole genome sequencing of cyanobacterium Nostoc sp. CCCryo 231-06 using microfluidic single cell technology

The Nostoc sp. strain CCCryo 231-06 is a cyanobacterial strain capable of surviving under extreme conditions and thus is of great interest for the astrobiology community. The knowledge of its complete genome sequence would serve as a guide for further studies. However, a major concern has been placed on the effects of contamination on the quality of sequencing data without a reference genome. Here, we report the use of microfluidic technology combined with single cell sequencing and de novo assembly to minimize the contamination and recover the complete genome of the Nostoc strain CCCryo 231-06 with high quality. 100% of the whole genome was recovered with all contaminants removed and a strongly supported phylogenetic tree. The data reported can be useful for comparative genomics for phylogenetic and taxonomic studies. The method used in this work can be applied to studies that require high-quality assemblies of genomes of unknown microorganisms.

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This work uses a microfluidic platform for Nostoc single cell sequencing

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This technology provides minimal contamination in single cell sequencing

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Complete genome of the Nostoc strain CCCryo 231-06 was recovered with high quality

Efficient estimation of stereo thresholds: What slope should be assumed for the psychometric function?

Bayesian staircases are widely used in psychophysics to estimate detection thresholds. Simulations have revealed the importance of the parameters selected for the assumed subject’s psychometric function in enabling thresholds to be estimated with small bias and high precision. One important parameter is the slope of the psychometric function, or equivalently its spread. This is often held fixed, rather than estimated for individual subjects, because much larger numbers of trials are required to estimate the spread as well as the threshold. However, if this fixed value is wrong, the threshold estimate can be biased. Here we determine the optimal slope to minimize bias and maximize precision when measuring stereoacuity with Bayesian staircases. We performed 2- and 4AFC disparity detection stereo experiments in order to measure the spread of the disparity psychometric function in human observers assuming a Logistic function. We found a wide range, between 0.03 and 3.5 log₁₀ arcsec, with little change with age. We then ran simulations to examine the optimal spread using the empirical data. From our simulations and for three different experiments, we recommend selecting assumed spread values between the percentiles 60–80% of the population distribution of spreads (these percentiles can be extended to other type of thresholds). For stereo thresholds, we recommend a spread around the value σ = 1.7 log₁₀ arcsec for 2AFC (slope β = 4.3 /log₁₀ arcsec), and around σ = 1.5 log₁₀ arcsec for 4AFC (β = 4.9 /log₁₀ arcsec). Finally, we compared a Bayesian procedure (ZEST using the optimal σ) with five Bayesian procedures that are versions of ZEST-2D, Psi, and Psi-marginal. In general, for the conditions tested, ZEST optimal σ showed the lowest threshold bias and highest precision.

Two choices good, four choices better: For measuring stereoacuity in children, a four-alternative forced-choice paradigm is more efficient than two

PURPOSE

Measuring accurate thresholds in children can be challenging. A typical psychophysical experiment is usually too long to keep children engaged. However, a reduction in the number of trials decreases the precision of the threshold estimate. We evaluated the efficiency of forced-choice paradigms with 2 or 4 alternatives (2-AFC, 4-AFC) in a disparity detection experiment. 4-AFC paradigms are statistically more efficient, but also more cognitively demanding, which might offset their theoretical advantage in young children.

METHODS

We ran simulations evaluating bias and precision of threshold estimates of 2-AFC and 4-AFC paradigms. In addition, we measured disparity thresholds in 43 children (aged 6 to 17 years) with a 4-AFC paradigm and in 49 children (aged 4 to 17 years) with a 2-AFC paradigm, both using an adaptive weighted one-up one-down staircase.

RESULTS

Simulations indicated a similar bias and precision for a 2-AFC paradigm with double the number of trials as a 4-AFC paradigm. On average, estimated threshold of the simulated data was equal to the model threshold, indicating no bias. The precision was improved with an increasing number of trials. Likewise, our data showed a similar bias and precision for a 2-AFC paradigm with 60 trials as for a 4-AFC paradigm with 30 trials. Trials in the 4-AFC paradigm took slightly longer as participants scanned more alternatives. However, the 4-AFC task still ended up faster for a given precision.

CONCLUSION

Bias and precision were similar in a 4-AFC task compared to a 2-AFC task with double the number of trials. However, a 4-AFC paradigm was more time efficient and is therefore recommended.

Contrast thresholds reveal different visual masking functions in humans and praying mantises

Recently, we showed a novel property of the Hassenstein–Reichardt detector, namely that insect motion detection can be masked by ‘undetectable’ noise, i.e. visual noise presented at spatial frequencies at which coherently moving gratings do not elicit a response (Tarawneh et al., 2017). That study compared the responses of human and insect motion detectors using different ways of quantifying masking (contrast threshold in humans and masking tuning function in insects). In addition, some adjustments in experimental procedure, such as presenting the stimulus at a short viewing distance, were necessary to elicit a response in insects. These differences offer alternative explanations for the observed difference between human and insect responses to visual motion noise. Here, we report the results of new masking experiments in which we test whether differences in experimental paradigm and stimulus presentation between humans and insects can account for the undetectable noise effect reported earlier. We obtained contrast thresholds at two signal and two noise frequencies in both humans and praying mantises (Sphodromantis lineola), and compared contrast threshold differences when noise has the same versus different spatial frequency as the signal. Furthermore, we investigated whether differences in viewing geometry had any qualitative impact on the results. Consistent with our earlier finding, differences in contrast threshold show that visual noise masks much more effectively when presented at signal spatial frequency in humans (compared to a lower or higher spatial frequency), while in insects, noise is roughly equivalently effective when presented at either the signal spatial frequency or lower (compared to a higher spatial frequency). The characteristic difference between human and insect responses was unaffected by correcting for the stimulus distortion caused by short viewing distances in insects. These findings constitute stronger evidence that the undetectable noise effect reported earlier is a genuine difference between human and insect motion processing, and not an artefact caused by differences in experimental paradigms.

Summary: We investigate alternative explanations for a reported difference between human and insect responses to masked moving gratings, and demonstrate that it is a genuine feature of their visual systems.

Overestimation of stereo thresholds by the TNO stereotest is not due to global stereopsis

PURPOSE

It has been repeatedly shown that the TNO stereotest overestimates stereo threshold compared to other clinical stereotests. In the current study, we test whether this overestimation can be attributed to a distinction between 'global' (or 'cyclopean') and 'local' (feature or contour-based) stereopsis.

METHODS

We compared stereo thresholds of a global (TNO) and a local clinical stereotest (Randot Circles). In addition, a global and a local psychophysical stereotest were added to the design. One hundred and forty-nine children between 4 and 16 years old were included in the study.

RESULTS

Stereo threshold estimates with TNO were a factor of two higher than with any of the other stereotests. No significant differences were found between the other tests. Bland-Altman analyses also indicated low agreement between TNO and the other stereotests, especially for higher stereo threshold estimates. Simulations indicated that the TNO test protocol and test disparities can account for part of this effect.

DISCUSSION

The results indicate that the global - local distinction is an unlikely explanation for the overestimated thresholds of TNO. Test protocol and disparities are one contributing factor. Potential additional factors include the nature of the task (TNO requires depth discrimination rather than detection) and the use of anaglyph red/green 3D glasses rather than polarizing filters, which may reduce binocular fusion.

The Stereoscopic Anisotropy Develops During Childhood

Purpose

Human vision has a puzzling stereoscopic anisotropy: horizontal depth corrugations are easier to detect than vertical depth corrugations. To date, little is known about the function or the underlying mechanism responsible for this anisotropy. Here, we aim to find out whether this anisotropy is independent of age. To answer this, we compare detection thresholds for horizontal and vertical depth corrugations as a function of age.

Methods

The depth corrugations were defined solely by the horizontal disparity of random dot patterns. The disparities depicted a horizontal or vertical sinusoidal depth corrugation of spatial frequency 0.1 cyc/deg. Detection thresholds were obtained using Bayesian adaptive staircases from a total of 159 subjects aged from 3 to 73 years. For each participant we computed the anisotropy index, defined as the log₁₀-ratio of the detection threshold for vertical corrugations divided by that for horizontal.

Results

Anisotropy index was highly variable between individuals but was positive in 87% of the participants. There was a significant correlation between anisotropy index and log-age (r = 0.21, P = 0.008) mainly driven by a significant difference between children and adults. In 67 children aged 3 to 13 years, the mean anisotropy index was 0.34 ± 0.38 (mean ± SD, meaning that vertical thresholds were on average 2.2 times the horizontal ones), compared with 0.59 ± 0.55 in 84 adults aged 18 to 73 years (vertical 3.9 times horizontal). This was mainly driven by a decline in the sensitivity to vertical corrugations. Children had poorer stereoacuity than adults, but had similar sensitivity to adults for horizontal corrugations and were actually more sensitive than adults to vertical corrugations.

Conclusions

The fact that adults show stronger stereo anisotropy than children raises the possibility that visual experience plays a critical role in developing and strengthening the stereo anisotropy.

The contrast sensitivity function of the praying mantis Sphodromantis lineola

The detection of visual motion and its direction is a fundamental task faced by several visual systems. The motion detection system of insects has been widely studied with the majority of studies focussing on flies and bees. Here we characterize the contrast sensitivity of motion detection in the praying mantis Sphodromantis lineola, an ambush predator that stays stationary for long periods of time while preying on fast-moving prey. In this, its visual behaviour differs from previously studied insects and we might therefore expect its motion detection system to differ from theirs. To investigate the sensitivity of the mantis we analyzed its optomotor response in response to drifting gratings with different contrasts and spatio-temporal frequencies. We find that the contrast sensitivity of the mantis depends on the spatial and temporal frequencies present in the stimulus and is separably tuned to spatial and temporal frequency rather than specifically to object velocity. Our results also suggest that mantises are sensitive to a broad range of velocities, in which they differ from bees and are more similar to hoverflies. We discuss our results in relation to the contrast sensitivities of other insects and the visual ecology of the mantis.

Synthesen und Strukturen sechsgliedriger Cyclometallaphosphazene von Tellur(IV) und Rhenium(VII) / Syntheses and Structures of Six-Membered Cyclometallaphosphazenes Containing Tellurium(IV) and Rhenium(VII)

The reactions of the tridentate ligands (Me3Si)2NC(4-RC6H4)NPPh,NSiMe3 [(1): R=H, (2): R=CF3] with Re2O7 yield the six-membered rings , (4): R=CF3]. The acyclic compound Me3SiNC(4-CF3C6H4)NPPh2NReO2OSiMe3 (5) has been obtained by reaction of 2 with Me3SiOReO3- 2 reacts quantitatively with TeCl4 to form the metallacycle . The molecular structures of 4·CH2Cl2 and 6 · pyridine · 0.5 toluene have been determined by X-ray diffraction.

Early evidence of increased risk for metabolic syndrome in young men with latent obstructive sleep apnea

BACKGROUND

Obstructive sleep apnea (OSA) is characterized by a repetitive collapse of the upper airway during sleep and may affect as many as 1 in 5 adults. Although OSA appears to increase risk for metabolic syndrome in middle-aged adults, no data currently exist in a younger, preclinical cohort.

METHODS

Forty-five sedentary young men: 12 overweight with OSA (OSA), 18 overweight without OSA (NOSA), and 15 normal-weight without OSA (CON). Respiratory distress index (RDI) was determined using an at-home, unsupervised, portable polygraphy device. Total and subcutaneous abdominal fat (SAF) were quantified using dual-energy X-ray absorptiometry (DXA). Blood pressure was obtained manually via auscultation. Fasting triglycerides, glucose, and high-density lipoprotein cholesterol (HDL-C) concentrations were analyzed from whole blood using a commercial lipid profile kit.

RESULTS

The OSA group had 25% more SAF than the NOSA group (P < 0.05) and higher triglycerides (136.7 +/- 21.3 mg/dL versus 92.2 +/- 7.5, P < 0.05). RDI was directly related to fasting triglycerides (R = 0.32, P < 0.05) after controlling for SAF. The number of metabolic syndrome components was directly correlated to indices of adiposity, but not RDI. Using multiple linear regression analysis, triglycerides were the only independent predictor of RDI.

CONCLUSIONS

Results from this study demonstrate that unique physiologic and anthropometric abnormalities exist in young men with occult OSA, beyond those that are seen in uncomplicated obesity. These findings may indicate early pathogenesis of metabolic syndrome in these young men.

Is new science driving practice improvements and better patient outcomes? Applications for cardiac rehabilitation

Evidence from many clinical trials in recent years suggests that a large "treatment gap" exists between recommended therapies and the care that patients actually receive. This gap has been particularly apparent in the area of primary and secondary prevention of cardiovascular disease. In this article, three areas are discussed in which new scientific advances have not been adequately translated to clinical practice. These include: 1) the most appropriate measures to define the risks associated with obesity; 2) the under-diagnosis of obstructive sleep apnea and its relation to cardiovascular risk; and 3) the use and misuse of the exercise test and other functional status tools to predict health outcomes. Each is discussed in terms of how they should be quantified, their contribution to the estimation of cardiovascular disease risk, their response to interventions, and implications for cardiac rehabilitation. Clinical cardiac rehabilitation programs can benefit from routinely including these measures, both for their value in stratifying risk and for their importance in quantifying program efficacy. Physicians and allied health professionals should expand their routine medical evaluations and coronary risk factor profiling to include these measures.

An isolated intracardiac echogenic focus as a marker for aneuploidy

OBJECTIVE

This study was undertaken to evaluate the relationship of an isolated fetal intracardiac echogenic focus in a population of patients with a mixed risk for aneuploidy when presenting for prenatal diagnosis.

STUDY DESIGN

All women referred to our institution for screening ultrasound were prospectively evaluated for the presence of an intracardiac echogenic focus in the fetal heart. Each patient was evaluated for the presence of clinical risk factors including ultrasound findings, biochemical screening, and maternal age. The population of patients was then described and neonatal outcomes were obtained.

RESULTS

A total of 10,875 patients were referred and 176 cases of fetal intracardiac echogenic foci were evaluated. There was an overall prevalence of 1.6% in our population. The patients with other ultrasound findings and/or maternal age older than 35 years who underwent amniocentesis had 3 abnormal karyotypes identified and had identifiable risk factors. In the group less than 35 years, the relative risk was 2.55 of having an amniocentesis for an isolated echogenic focus (with no cases of fetal aneuploidy found) in comparison with our referred group of nonadvanced maternal age patients without any ultrasound markers or findings.

CONCLUSION

This isolated echogenic finding appears to be a benign variant and not an increased risk for fetal aneuploidy. The chromosomal abnormalities were seen in the group with risk factors including maternal age and/or other ultrasound findings. Evaluation of maternal age, biochemical markers, and ultrasound markers should be used together to help determine the risk of patients with an isolated echogenic focus.

Low compliance with national standards for cardiovascular emergency preparedness at health clubs

There is heightened concern that older adults and individuals with occult or known heart disease are exercising at fitness facilities that do not provide adequate cardiovascular screening and emergency procedures, as outlined in contemporary recommendations. To evaluate adherence to these standards, we surveyed 122 randomly chosen fitness clubs in Ohio (53% response rate; n = 65) that included > 110,000 total members. Special programs for older adults, cardiac patients, or both, were offered at 52% of these clubs. More than one fourth of the clubs (28%) failed to employ pre-entry screening to identify members with signs, symptoms, or history of cardiovascular disease, even though 17% reported one or more cardiovascular emergencies (ie, acute myocardial infarction, sudden cardiac death, or both) in their facility during the past 5 years. Moreover, a majority of the clubs (53%) had no written emergency response plan and 92% failed to conduct emergency response drills as described in published national standards. Only 3% of the centers reported having automated external defibrillators. These findings indicate that staff at public fitness facilities must work to identify members with signs, symptoms, or history of cardiovascular disease and prepare for prompt and appropriate responses to cardiovascular emergencies as described in contemporary national recommendations. Such risk management procedures may reduce exercise-related cardiovascular events among the escalating number of moderate-to-high-risk adults who are being mainstreamed into health and fitness facilities.

A nomogram to predict exercise capacity from a specific activity questionnaire and clinical data

Recent investigations suggested that clinical exercise testing can be optimized by individualizing the protocol, depending on the purpose of the test and the subject tested. This requires some knowledge of a patient's exercise capacity before beginning the test. The accuracy of a simple physical activity questionnaire and readily available clinical data in predicting subsequent treadmill performance was examined. A brief, self-administered questionnaire (VSAQ) was developed for veterans who were referred to exercise testing for clinical reasons. The VSAQ was designed to determine which specific daily activities were associated with symptoms of cardiovascular disease (fatigue, chest pain and shortness of breath). Two hundred twelve consecutive patients (mean age 62 +/- 8 years) referred for maximal exercise testing were studied. Clinical and demographic variables were added to VSAQ responses in a stepwise regression model to determine their ability to predict treadmill performance. Only metabolic equivalents by VSAQ, and age were significant predictors of treadmill performance; these 2 variables yielded R = 0.82 (SEE 1.43; p < 0.001), and explained 67% of the variance in exercise capacity. The regression equation reflecting the relation between age, VSAQ and exercise capacity was: achieved metabolic equivalents = 4.7 + 0.97 (VSAQ) - 0.06 (age). Using this equation, a nomogram was developed. Incorporating the VSAQ with the nomogram requires only a few minutes, and yields a reasonably accurate estimate of a patient's exercise capacity. Although the present equation is population-specific, a similar approach in different populations may be useful for individualizing protocols for clinical exercise testing.

Chromosome mosaicism in 6,000 amniocenteses

Multiple cell-multiple flask mosaicism was found in 0.20% of 6,000 amniocenteses, and multiple cell-single flask mosaicism was found in 0.92%. Multiple cell-multiple flask mosaicism usually was found in fetal or infant tissues at delivery or elective abortion. Most multiple cell-multiple flask mosaicism involved sex chromosomes and was either 45, X/46, XY or 45, X/46, XX. Except for one fetus with 45, X/46, XX and an aortic coarctation, phenotypic abnormalities associated with sex chromosome mosaicism were not found in these patients. One normal boy has continued to show 45,X mosaicism during the first 4 years of life. Autosome abnormalities found in multiple cell-multiple flask mosaicism included del(18q) associated with fetal anomalies. Apparently normal phenotypes were associated with prenatal trisomy 17, two de novo supernumerary marker chromosomes, and monosomy 21. Since an aberrant cell line present in only one primary amniotic fluid cell culture was occasionally identified from another amniocentesis or at birth, multiple cell-single flask mosaicism involving a sex chromosome or a viable autosome abnormality cannot be assumed to be an in vitro event. Maternal cell contamination, which was found in 0.49% of amniocenteses, could have resulted in an erroneous diagnosis of fetal sex in two cases if cells from independent culture vessels were not examined.

Role of amniocentesis in ultrasound-detected fetal malformations

Sixty-three patients with antenatally diagnosed fetal malformations over the period of 14 months were prospectively offered genetic amniocentesis, irrespective of gestational age. An additional 15 patients were excluded from the study because of a known lethal malformation (13 anencephaly, two amniotic bands). Twenty patients accepted amniocentesis, and seven chromosomal disorders were found. Obstetric management was altered in some of these patients as a result of the anomalies.